Identification and cloning of a lettuce albino mutation through whole-genome resequencing

Keywords

Lettuce / ⁶⁰Co γ-irradiation / BSR-seq / Albino mutant

References

[1] Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, et al.. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol, 2012, 30: 174-178

[2] An G, Qi Y, Zhang W, Gao H, Qian J, Larkin RM, et al.. LsNRL4 enhances photosynthesis and decreases leaf angles in lettuce. Plant Biotechnol J, 2022, 20: 1956-1967

[3] Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 2014, 30: 2114-2120

[4] Bull T, Debernardi J, Reeves M, Hill T, Bertier L, Van Deynze A, et al.. GRF-GIF chimeric proteins enhance in vitro regeneration and Agrobacterium-mediated transformation efficiencies of lettuce (Lactuca spp.). Plant Cell Rep, 2023, 42: 629-643

[5] Bürstenbinder K, Möller B, Plötner R, Stamm G, Hause G, Mitra D, et al.. The IQD family of calmodulin-binding proteins links calcium signaling to microtubules, membrane subdomains, and the nucleus. Plant Physiol, 2017, 173: 1692-1708

[6] Dutta S, Hazra P, Saha S, Acharya B, Bhattacharjee T, Kumar Maurya P, et al. Applied mutagenesis could improve economically important traits in bitter gourd (Momordica charantia L.). J Genet. 2021;100:43. https://doi.org/10.1007/s12041-021-01283-5.

[7] Emerson R. Chlorophyll content and rate of photosynthesis. Proc Natl Acad Sci U S A, 1929, 15: 281-284

[8] Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H, et al.. Mutmap⁺: Genetic mapping and mutant identification without crossing in rice. PLoS ONE, 2013, 8 e68529

[9] Feng JX, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y. GFOLD: A generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics, 2012, 28: 2782-2788

[10] Gurdon C, Poulev A, Armas I, Satorov S, Tsai M, Raskin I. Genetic and phytochemical characterization of lettuce flavonoid biosynthesis mutants. Sci Rep, 2019, 9 3305

[11] Gurdon C, Kozik A, Tao R, Poulev A, Armas I, Michelmore RW, et al.. Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family. Plant Physiol, 2021, 186: 929-944

[12] He W, Zhao S, Liu X, Dong S, Lv J, Liu D, et al.. Reseqtools: An integrated toolkit for large-scale next-generation sequencing based resequencing analysis. Genet Mol Res, 2013, 12: 6275-6283

[13] Huang CC, Lin CH, Lin YC, Chang HX. Application of bulk segregant RNA-Seq (BSR-Seq) and allele-specific primers to study soybean powdery mildew resistance. BMC Plant Biol, 2024, 24 155

[14] Ito D, Yoshimura K, Ishikawa K, Ogawa T, Maruta T, Shigeoka S. A comparative analysis of the molecular characteristics of the Arabidopsis CoA pyrophosphohydrolases AtNUDX11, 15, and 15a. Biosci Biotechnol Biochem, 2012, 76: 139-147

[15] Kendig KI, Baheti S, Bockol MA, Drucker TM, Hart SN, Heldenbrand JR, et al.. Sentieon DNASeq variant calling workflow demonstrates strong computational performance and accuracy. Front Genet, 2019, 10: 736

[16] Kurtar ES, Balkaya A, Kandemir D. Determination of semi-lethal (LD50) doses for mutation breeding of Turkish winter squash (Cucurbita maxima Duch.) and pumpkin (Cucurbita moschata Duch.). Fresenius Environ Bull. 2017;26:3209–16. https://hdl.handle.net/20.500.12712/12847.

[17] Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 2009, 10 R25

[18] Larkin RM, Alonso JM, Ecker JR, Chory J. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science, 2003, 299: 902-906

[19] Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. Plant J, 2022, 109: 1355-1374

[20] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al.. The Sequence Alignment/Map format and SAMtools. Bioinformatics, 2009, 25: 2078-2079

[21] Li R, Hou Z, Gao L, Xiao D, Hou X, Zhang C, et al.. Conjunctive analyses of BSA-Seq and BSR-seq to reveal the molecular pathway of leafy head formation in Chinese cabbage. Plants, 2019, 8 603

[22] Li Z, Chen X, Shi S, Zhang H, Wang X, Chen H, et al.. DeepBSA: a deep-learning algorithm improves bulked segregant analysis for dissecting complex traits. Mol Plant, 2022, 15: 1418-1427

[23] Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen LL. CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome editing in plants. Mol Plant, 2017, 10: 530-532

[24] Liu X, Cheng X, Cao J, Zhu W, Sun Y, Lin N, et al.. UV-B regulates seasonal greening of albino leaves by modulating CsHY5-inhibiting chlorophyll biosynthesis in Camellia sinensis cv. Huangkui Plant Sci, 2023, 328 111569

[25] Liu H, Xiong Z, Chen Q, Wang L, Wang C. Study on the preservation effect of ⁶⁰Co-γ ray irradiation on potatoes. Sci Rep, 2024, 14: 21811

[26] Ma Q, Li H, Zou Z, Arkorful E, Lv Q, Zhou Q, et al.. Transcriptomic analyses identify albino-associated genes of a novel albino tea germplasm 'Huabai 1'. Hortic Res, 2018, 5: 54

[27] McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al.. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res, 2010, 20: 1297-1303

[28] Peter E, Grimm B. GUN4 is required for posttranslational control of plant tetrapyrrole biosynthesis. Mol Plant, 2009, 2: 1198-1210

[29] Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C, et al.. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun, 2017, 8: 14953

[30] Sandhu D, Coleman Z, Atkinson T, Rai KM, Mendu V. Genetics and physiology of the nuclearly inherited yellow foliar mutants in soybean. Front Plant Sci, 2018, 9: 471

[31] Sikder S, Biswas P, Hazra P, Akhtar S, Chattopadhyay A, Badigannavar AM, et al.. Induction of mutation in tomato (Solanum lycopersicum L.) by gamma irradiation and EMS. Indian J Genet Plant Breed, 2013, 73: 392-399

[32] Su W, Tao R, Liu W, Yu C, Yue Z, He S, et al.. Characterization of four polymorphic genes controlling red leaf colour in lettuce that have undergone disruptive selection since domestication. Plant Biotechnol J, 2020, 18: 479-490

[33] Takagi H, Uemura A, Yaegashi H, Tamiru M, Abe A, Mitsuoka C, et al.. MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. New Phytol, 2013, 200: 276-283

[34] Tanaka A, Tanaka R. Chlorophyll metabolism. Curr Opin Plant Biol, 2006, 9: 248-255

[35] Terauchi R, Abe A, Takagi H, Yoshida K, Kosugi S, Natsume S, et al.. Whole genome sequencing and future breeding of rice. J Plant Biochem Biotechnol, 2012, 21: 10-14

[36] Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, et al.. AgriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res, 2017, 45: W122-W129

[37] Wang X, Han L, Li J, Shang X, Liu Q, Li L, et al.. Next-generation bulked segregant analysis for breeding 4.0. Cell Rep, 2023, 42 113039

[38] Wang Y, Li X, Liu M, Zhou Y, Li F. Guide RNA scaffold variants enabled easy cloning of large gRNA cluster for multiplexed gene editing. Plant Biotechnol J, 2024, 22: 460-471

[39] Yang C, Zhu J, Jiang Y, Wang X, Gu M, Wang Y, et al.. 100 Gy ⁶⁰Co γ-ray induced novel mutations in tetraploid wheat. Sci World J, 2014, 2014 725813

[40] Ye S, Yan L, Ma X, Chen Y, Wu L, Ma T, et al.. Combined BSA-Seq based mapping and RNA-Seq profiling reveal candidate genes associated with plant architecture in Brassica napus. Int J Mol Sci, 2022, 23 2472

[41] Yin L, Hou Y, Chen X, Huang X, Feng M, Wang C, et al.. Construction of watermelon mutant library based on ⁶⁰Co γ-ray irradiation and EMS treatment for germplasm innovation. Horticulturae, 2023, 9: 1133

[42] Zhang L, Su W, Tao R, Zhang W, Chen J, Wu P, et al.. RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. Nat Commun, 2017, 8: 2264

[43] Zhang JY, Wang T, Jia ZH, Guo ZR, Liu YZ, Wang G. Photosystem disorder could be the key cause for the formation of albino leaf phenotype in pecan. Int J Mol Sci, 2020, 21 6137

[44] Zhang L, Qian J, Han Y, Jia Y, Kuang H, Chen J. Alternative splicing triggered by the insertion of a CACTA transposon attenuates LsGLK and leads to the development of pale‐green leaves in lettuce. Plant J, 2021, 109: 182-195

[45] Zhang Q, Li C, Jiao Z, Ruan J, Liu MY. Integration of metabolomics and transcriptomics reveal the mechanism underlying accumulation of flavonols in albino tea leaves. Molecules, 2022, 27 5792

[46] Zhang H, Zhang W, Xiang F, Zhang Z, Guo Y, Chen T, et al.. Photosynthetic characteristics and genetic mapping of a new yellow leaf mutant crm1 in Brassica napus. Mol Breed, 2023, 43 80

[47] Zhang X, Liang X, He S, Tian H, Liu W, Jia Y, et al.. Seed color in lettuce is determined by the LsTT2, LsCHS, and Ls2OGD genes from the flavonoid biosynthesis pathway. Theor Appl Genet, 2023, 136: 241

[48] Zhang M, Song M, Cheng F, Han X, Cheng C, Yu X, et al.. The mutation of ent-kaurenoic acid oxidase, a key enzyme involved in gibberellin biosynthesis, confers a dwarf phenotype to cucumber. Theor Appl Genet, 2025, 138 12

[49] Zuo DP, Wang B, Liu YZ, Chen ZS, Hu RJ, He MJ, et al.. A triose phosphate/phosphate translocator triggers antimicrobial immunity by exporting glyceraldehyde 3-phosphate from chloroplasts. Plant Cell, 2025, 37 koaf245

Funding

Natural Science Foundation of Qinghai Province(2025-ZJ-968T)

Rights & permissions

The Author(s)